Diversity and composition of bacterial endophytes among plant parts of  Panax notoginseng

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Abstract

Background

Bacterial endophytes are widespread inhabitants inside plant tissues that play crucial roles in plant growth and biotransformation. This study aimed to offer information for the exploitation of endophytes by analyzing the bacterial endophytes in different parts of Panax notoginseng.

Methods

We used high-throughput sequencing methods to analyze the diversity and composition of bacterial endophytes from different parts of P. notoginseng.

Results

A total of 174,761 classified sequences were obtained from the analysis of 16S ribosomal RNA in different parts of P. notoginseng. Its fibril displayed the highest diversity of bacterial endophytes. Principal coordinate analysis revealed that the compositions of the bacterial endophytes from aboveground parts (flower, leaf, and stem) differed from that of underground parts (root and fibril). The abundances of Conexibacter, Gemmatimonas, Holophaga, Luteolibacter, Methylophilus, Prosthecobacter, and Solirubrobacter were significantly higher in the aboveground parts than in the underground parts, whereas the abundances of Bradyrhizobium, Novosphingobium, Phenylobacterium, Sphingobium, and Steroidobacter were markedly lower in the aboveground parts.

Conclusions

Our results elucidated the comprehensive diversity and composition profiles of bacterial endophytes in different parts of 3-year-old P. notoginseng. Our data offered pivotal information to clarify the role of endophytes in the production of P. notoginseng and its important metabolites.

Electronic supplementary material

The online version of this article (10.1186/s13020-018-0198-5) contains supplementary material, which is available to authorized users.

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Most cited references 38

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Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays.

Noah Fierer, Jason Jackson, Rytas Vilgalys … (2005)

Here we describe a quantitative PCR-based approach to estimating the relative abundances of major taxonomic groups of bacteria and fungi in soil. Primers were thoroughly tested for specificity, and the method was applied to three distinct soils. The technique provides a rapid and robust index of microbial community structure.

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Bacterial Communities Associated with the Leaves and the Roots of Arabidopsis thaliana

Natacha Bodenhausen, Matthew Horton, Joy Bergelson (2013)

Diverse communities of bacteria inhabit plant leaves and roots and those bacteria play a crucial role for plant health and growth. Arabidopsis thaliana is an important model to study plant pathogen interactions, but little is known about its associated bacterial community under natural conditions. We used 454 pyrosequencing to characterize the bacterial communities associated with the roots and the leaves of wild A. thaliana collected at 4 sites; we further compared communities on the outside of the plants with communities in the endophytic compartments. We found that the most heavily sequenced bacteria in A. thaliana associated community are related to culturable species. Proteobacteria, Actinobacteria, and Bacteroidetes are the most abundant phyla in both leaf and root samples. At the genus level, sequences of Massilia and Flavobacterium are prevalent in both samples. Organ (leaf vs root) and habitat (epiphytes vs endophytes) structure the community. In the roots, richness is higher in the epiphytic communities compared to the endophytic compartment (P = 0.024), while the reverse is true for the leaves (P = 0.032). Interestingly, leaf and root endophytic compartments do not differ in richness, diversity and evenness, while they differ in community composition (P = 0.001). The results show that although the communities associated with leaves and roots share many bacterial species, the associated communities differ in structure.

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Biofertilizers: a potential approach for sustainable agriculture development.

Prosun Tribedi, Abhrajyoti Ghosh, Bannhi Das … (2017)

The worldwide increase in human population raises a big threat to the food security of each people as the land for agriculture is limited and even getting reduced with time. Therefore, it is essential that agricultural productivity should be enhanced significantly within the next few decades to meet the large demand of food by emerging population. Not to mention, too much dependence on chemical fertilizers for more crop productions inevitably damages both environmental ecology and human health with great severity. Exploitation of microbes as biofertilizers is considered to some extent an alternative to chemical fertilizers in agricultural sector due to their extensive potentiality in enhancing crop production and food safety. It has been observed that some microorganisms including plant growth promoting bacteria, fungi, Cyanobacteria, etc. have showed biofertilizer-like activities in the agricultural sector. Extensive works on biofertilizers have revealed their capability of providing required nutrients to the crop in sufficient amounts that resulted in the enhancement of crop yield. The present review elucidates various mechanisms that have been exerted by biofertilizers in order to promote plant growth and also provides protection against different plant pathogens. The aim of this review is to discuss the important roles and applications of biofertilizers in different sectors including agriculture, bioremediation, and ecology.

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Author and article information

Contributors

Linlin Dong: lldong@icmm.ac.cn

Ruiyang Cheng: rycheng@icmm.ac.cn

Lina Xiao: 425113948@qq.com

Fugang Wei: weifugang@live.com

Guangfei Wei: 874101744@qq.com

Jiang Xu: jxu@icmm.ac.cn

Yong Wang: ws-wangyong37@163.com

Xiaotong Guo: guoxtina@126.com

Zhongjian Chen: panaxnotoginseng@126.com

Shilin Chen: 0086-10-57203877 , slchen@icmm.ac.cn

Journal

Journal ID (nlm-ta): Chin Med

Journal ID (iso-abbrev): Chin Med

Title: Chinese Medicine

Publisher: BioMed Central (London )

ISSN (Electronic): 1749-8546

Publication date (Electronic): 14 August 2018

Publication date PMC-release: 14 August 2018

Publication date Collection: 2018

Volume: 13

Electronic Location Identifier: 41

Affiliations

[1 ]ISNI 0000 0004 0632 3409, GRID grid.410318.f, Institute of Chinese Materia Medica, , China Academy of Chinese Medical Sciences, ; Beijing, 100700 China

[2 ]Wenshan Miaoxaing Notoginseng Technology, Co., Ltd., Wenshan, 663000 China

[3 ]ISNI 0000 0004 1756 0485, GRID grid.460126.7, Institute of Sanqi Research, , Wenshan University, ; Wenshan, 663000 China

[4 ]GRID grid.443651.1, College of Agriculture, , Ludong University, ; Yantai, 264025 China

Article

Publisher ID: 198

DOI: 10.1186/s13020-018-0198-5

PMC ID: 6092820

PubMed ID: 30127840

SO-VID: 48d6cae6-6de2-466a-9850-abddb713b1f0

License:

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

History

Date received : 28 May 2018

Date accepted : 26 July 2018

Funding

Funded by: the Fundamental Research Funds for the Central public welfare research institutes

Award ID: ZXKT17049

Award Recipient : Linlin Dong

Funded by: FundRef http://dx.doi.org/10.13039/501100005090, Beijing Nova Program;

Award ID: Z181100006218020

Award Recipient : Linlin Dong

Funded by: the Major Science and Technology Programs in Yunnan Province

Award ID: 2016ZF001-001

Award Recipient : Linlin Dong

Funded by: the Science and Technology Project of Yantai

Award ID: 2015ZH071

Award Recipient : Xiaotong Guo

Custom metadata

ScienceOpen disciplines: Complementary & Alternative medicine

Keywords: panax notoginseng,endophytes,plant parts,high-throughput sequencing,16s ribosomal rna

Data availability:

ScienceOpen disciplines: Complementary & Alternative medicine

Keywords: panax notoginseng, endophytes, plant parts, high-throughput sequencing, 16s ribosomal rna

Diversity and composition of bacterial endophytes among plant parts of Panax notoginseng

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Abstract

Background

Methods

Results

Conclusions

Electronic supplementary material

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The International Journal of Person Centered Medicine

Most cited references 38

Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays.

Bacterial Communities Associated with the Leaves and the Roots of Arabidopsis thaliana

Biofertilizers: a potential approach for sustainable agriculture development.

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